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Number of items: 135. 2022Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished) Zafferi, Andrea and Huber, Konstantin and Peschka, Dirk and Vrijmoed, Johannes and John, Timm and Thomas, Marita (2022) A porous-media model for reactive fluid-rock interaction. Preprint . (Unpublished) 2021Mikula, Natalia and Dörffel, Tom and Baum, Daniel and Hege, Hans-Christian (2021) An Interactive Approach for Identifying Structure Definitions. arXive . pp. 1-29. (Submitted) Heida, Martin and Kantner, Markus and Stephan, Artur (2021) Consistency and convergence for a family of finite volume discretizations of the Fokker--Planck operator. ESAIM: Mathematical Modelling and Numerical Analysis, 55 . pp. 3017-3042. (Submitted) Dörffel, Tom and Papke, Ariane and Klein, Rupert and Ernst, Natalia and Smolarkiewicz, Piotr K. (2021) Dynamics of tilted atmospheric vortices under asymmetric diabatic heating. Theoretical and Computational Fluid Dynamics . Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2021) The Dynamic State Index with Moisture and Phase Changes. J. Math. Phys, 62 (12). pp. 1-12. Straube, Arthur V. and Winkelmann, Stefanie and Schütte, Christof and Höfling, Felix (2021) Stochastic pH Oscillations in a Model of the Urea−Urease Reaction Confined to Lipid Vesicles. J. Phys. Chem. Lett., 12 . pp. 1-6. Heida, Martin and Thomas, Marita (2021) GENERIC for dissipative solids with bulk-interface interaction. wias preprint . pp. 1-27. ISSN 2198-5855 (Submitted) Mielke, Alexander and Peletier, Mark A. and Stephan, Artur (2021) EDP-convergence for nonlinear fast–slow reaction systems with detailed balance. Nonlinearity 34 (, 34 . pp. 5762-5798. Thomas, Marita and Tornquist, Sven (2021) Discrete approximation of dynamic phase-field fracture in visco-elastic materials. Discrete Contin. Dyn. Syst. Ser. S, 14 . pp. 3865-3924. Zafferi, Andrea and Peschka, Dirk and Thomas, Marita (2021) GENERIC framework for reactive fluid flows. Preprint (2841). pp. 1-75. ISSN 2198-5855 (Submitted) Zendehroud, Sina and Netz, Roland R. and Kappler, Julian (2021) Linear Waves at Viscoelastic Interfaces Between Viscoelastic Media. Physical Review Fluids . pp. 1-19. (Submitted) Klein, Rupert and Viand, R. E. and Höfling, Felix and Delle Site, Luigi (2021) Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests. Advanced Theory and Simulations, 4 . pp. 1-10. Mielke, Alexander and Montefusco, Alberto and Peletier, Mark A. (2021) Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence. Continuum Mechanics and Thermodynamics, 33 (2). pp. 611-637. Frömberg, Daniela and Höfling, Felix (2021) Generalized master equation for first-passage problems in partitioned spaces. Journal of Physics A, 54 (21). pp. 1-29. Klein, Rupert and Schielicke, Lisa and Pfahl, Stephan and Khouider, Boualem (2021) QG-DL: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences . pp. 1-12. ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) Mielke, Alexander and Netz, Roland R. and Zendehroud, Sina (2021) A rigorous derivation and energetics of a wave equation with fractional damping. Journal Evolution Equations, 21 . pp. 3079-3102. Andreis, Luisa and König, Wolfgang and Patterson, Robert I.A. (2021) A large‐deviations principle for all the cluster sizes of a sparse Erdős–Rényi graph. Random Structures and Algorithms . pp. 1-32. Patterson, Robert I.A. and Renger, D.R. Michiel and Sharma, Upanshu (2021) Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective. arXive . pp. 1-47. (Unpublished) Kaatz, Lisa and Zertani, Sascha and Moulas, Evangelos and John, Timm and Labrousse, Loïc and Schmalholz, Stefan M. and Andersen, Torgeir B. (2021) Widening of Hydrous Shear Zones During Incipient Eclogitization of Metastable Dry and Rigid Lower Crust— Holsnøy, Western Norway. Tectonics, 40 (3). pp. 1-19. ISSN 1944-9194 Golami, Abbas and Höfling, Felix and Klein, Rupert and Delle Site, Luigi (2021) Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. Advanced Theory and Simulations, 4 . pp. 1-10. Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I.A. and Renger, D.R. Michiel (2021) LARGE DEVIATIONS FOR MARKOV JUMP PROCESSES WITH UNIFORMLY DIMINISHING RATES. arXive . pp. 1-19. (Unpublished) Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I. A. and Renger, D.R. Michiel (2021) Large deviations for Markov jump processes with uniformly diminishing rates. arXive . pp. 1-19. (Unpublished) Nüsken, N. and Renger, M. (2021) Stein Variational Gradient Descent: many-particle and long-time asymptotics. arXive . pp. 1-25. (Unpublished) Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) Stochastic homogenization of Λ-convex gradient flows. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS SERIES S, 14 (1). pp. 427-459. Renger, D.R. Michiel and Zimmer, Johannes (2021) Orthogonality of fluxes in general nonlinear reaction networks. DCDS-S 2021, 14 (1). pp. 205-217. (Submitted) Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) STOCHASTIC HOMOGENIZATION OF �-CONVEX GRADIENT FLOWS. Discrete and Continuous Dynamical Systems - S, 14 (1). pp. 1-27. Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2021) QG-DL-Ekman: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences . (In Press) Tierno, Pietro and Johansen, Tom H. and Straube, Arthur V. (2021) Thermally active nanoparticle clusters enslaved by engineered domain wall traps. NATURE COMMUNICATIONS, 12 (5813). pp. 1-11. 2020Mielke, Alexander and Maas, Jan (2020) Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics, 181 . pp. 2257-2303. Delle Site, L. and Klein, R. and Höfling, F. and Viand, R. E. (2020) Theory and simulation of open systems out of equilibrium. J. Chem. Phys. (2020);, 153 (10). pp. 1-7. ISSN 101102 Delle Site, L. and Klein, R. (2020) Liouville-type equations for the n-particle distribution functions of an open system. Journal of Mathematical Physics, 61 (8). Franchi, Bruno and Heida, Martin and Lorenzani, Silvia (2020) A Mathematical model for Alzheimer's disease: An approach via stochastic homogenization of the Smoluchowski equation. Communications in Mathematical Sciences, 18 (4). pp. 1105-1134. Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2020) Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures. Communications Physics, 3 (126). pp. 1-11. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2020) Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes. Nonlinearity, 33 (7). pp. 3206-3236. Soucek, Ondrej and Heida, Martin and Malek, Josef (2020) On a thermodynamic framework for developing boundary conditions for Korteweg-type fluids. International Journal of Engineering Science, 154 . pp. 1-28. Beinlich, A. and John, T. and Vrijmoed, J.C. and Tominaga, M. and Podladchikov, Y.Y. (2020) Instantaneous rock transformations in the deep crust driven by reactive fluid flow. nature geoscience, 13 . pp. 307-311. Heida, M. and Kornhuber, R. and Podlesny, J. (2020) Fractal homogenization of multiscale interface problems. Multiscale Modeling & Simulation, 18 (1). pp. 294-314. ISSN 1540-3459 Gussmann, P. and Mielke, A. (2020) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Advances in Calculus of Variations . Delle Site, L. and Praprotnik, M. and Bell, J. B. and Klein, R. (2020) Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Simulation, 3, 1900232 (2020), 3 (190023). pp. 1-20. Flegel, Franziska and Heida, Martin (2020) The fractional p-Laplacian emerging from homogenization of the random conductance model with degenerate ergodic weights and unbounded-range jumps. Calculus of Variations and Partial Differential Equations, 59 (8). (Unpublished) Mielke, Alexander and Stephan, Artur (2020) Coarse-graining via EDP-convergence for linear fast-slow reaction systems. Mathematical Models and Methods in Applied Sciences, 30 (9). pp. 1765-1807. 2019Bartscha, Clemens and Wiedmeyer, Viktoria and Lakdawala, Zahra and Patterson, Robert I.A. and Voigt, Andreas and Sundmacher, Kai and John, Volker (2019) Stochastic-deterministic population balance modeling and simulation of a fluidized bed crystallizer experiment. Chemical Engineering Science, 208 . ISSN 115102 Chen, Shuo and Hin, Remco C. and John, Timm and Bryan, Ben and Nui, Yaoling and Elliott, Tim and Brooker, R. (2019) Molybdenum systematics of subducted crust record reactive fluid flow from underlying slab serpentine dehydration. nature communications . pp. 1-9. Patterson, R. I. A and Renger, M. (2019) Large deviations of jump process fluxes. Math. Phys. Anal. Geom., 22 (21). pp. 1-32. ISSN 1385-0172; ESSN: 1572-9656 Flegel, Franziska and Heida, Martin and Slowik, Martin (2019) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. Ann. Inst. H. Poincaré Probab. Statist., 55 (3). pp. 1226-1257. Flegel, Franziska and Heida, Martin and Slowik, Martin (2019) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. Annales de l Institut Henri Poincaré Probabilités et Statistiques, 55 (3). pp. 1226-1257. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2019) "Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes" by Hittmeir, Sabine; Klein, Rupert; Li, Jinkai; Titi, Edriss. Analysis of PDEs . pp. 1-28. ISSN 1907.11199 (Submitted) Renger, M. and Zimmer, J. (2019) Orthogonality of fluxes in general nonlinear reaction networks. SFB1114 Preprint 07/2019 in WIAS No. 2609 . pp. 1-12. (Unpublished) Bartsch, Clemens and John, Volker and Patterson, Robert I. A. (2019) Simulations of an ASA flow crystallizer with a coupled stochastic-deterministic approach. Computers & Chemical Engineering, 124 . pp. 350-363. Heida, M. and Nesenenko, S. (2019) Stochastic homogenization of rate-dependent models of monotone type in plasticity. Asymptotic Analysis, 112 (3-4). pp. 185-212. ISSN 0921-7134 Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 0021-9606, ESSN: 1089-7690 Pinamonti, G. and Paul, F. and Noé, F. and Rodriguez, A. and Bussi, G. (2019) The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 0021-9606, ESSN: 1089-7690 Wang, J. and Olsson, S. and Wehmeyer, C. and Perez, A. and Charron, N.E. and de Fabritiis, G. and Noé, F. and Clementi, C. (2019) Machine Learning of coarse-grained Molecular Dynamics Force Fields. ACS Cent. Sci., 5 (5). pp. 755-767. ISSN 2374-7943, ESSN: 2374-7951 Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul, 2 (5). Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished) Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 1553-7358 Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848 Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 0021-9606, ESSN: 1089-7690 Peschka, D. and Thomas, M. and Ahnert, T. and Münch, A. and Wagner, B. (2019) Gradient structures for flows of concentrated suspensions. Topics in Applied Analysis and Optimisation . pp. 295-318. 2018Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogen-bond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). -244504. ISSN 0021-9606, ESSN: 1089-7690 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690 Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524 Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 1-22. ISSN 2353-6438 (online) Heida, M. and Patterson, R. I. A and Renger, M. (2018) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. J. Evol. Equ. . pp. 1-42. ISSN Online: 1424-3202 Print: 1424-3199 Heida, M. (2018) Convergences of the squareroot approximation scheme to the Fokker–Planck operator. Mathematical Models and Methods in Applied Sciences, 28 (13). pp. 2599-2635. ISSN 0218-2025, ESSN: 1793-6314 Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 1261-1326. ISSN 0022-4715 Fröhner, Chr. and Noé, F. (2018) Reversible interacting-particle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 11240-11250. Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690 del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). 044102. ISSN 0021-9606, ESSN: 1089-7690 Dibak, M. and del Razo, M.J. and De Sancho, D. and Schütte, Ch. and Noé, F. (2018) MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 0021-9606 Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 1915-1957. ISSN 1432-1467 (online) Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 1-29. (Unpublished) Heida, Martin and Röger, Matthias (2018) Large deviation principle for a stochastic Allen--Cahn equation. Journal of Theoretical Probability 31(1), 31 (1). pp. 1-18. (Submitted) Schulz, R. and Hansen, Y. von and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water. SFB 1114 Preprint 02/2018 . (Unpublished) Heida, Martin and Schweizer, Ben (2018) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations, 24 (1). 153 -176. Dondl, Patrick and Frenzel, Thomas and Mielke, Alexander (2018) A gradient system with a wiggly energy and relaxed EDP-convergence. ESAIM Control Optimisation and Calculus of Variations, 25 . pp. 1-46. (Submitted) Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690 Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137-164. ISSN 0935-4964 (Print) 1432-2250 (Online) Liero, M. and Mielke, A. and Savaré, G. (2018) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Inventiones mathematicae, 211 . pp. 969-1117. ISSN 1432-1297 (online) Mielke, Alexander and Mittnenzweig, Markus (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science, 28 . pp. 765-806. ISSN 1432-1467 (online) 2017Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) Kappler, J. and Shrivastava, S. and Schneider, M.F. and Netz, R.R. (2017) Nonlinear fractional waves at elastic interfaces. Phys. Rev. Fluids, 2 (11). p. 114804. Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690 Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095). Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global well-posedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715 Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084 Heida, M. (2017) Stochastic homogenization of rate-independent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853-894. ISSN 1432-0959 (online) 0935-1175 (print) Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and Blume-Peytavi, U. and Hedtrich, S. and Schäfer-Korting, M. and Rühl, E. and Netz, R.R. (2017) Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles. PNAS, 114 (14). pp. 3631-3636. ISSN 1091-6490 (online) Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2017) On microscopic origins of generalized gradient structures. Discrete and Continuous Dynamical Systems - Series S, 10 (1). Heida, M. and Mielke, A. (2017) Averaging of time-periodic dissipation potentials in rate-independent processes. Discrete and Continuous Dynamical Systems - Series S, 10 (6). pp. 1303-1327. Mielke, A. (2017) Three examples concerning the interaction of dry friction and oscillations. In: Trends on Application of Mathematics to Mechanics. Springer Proceedings of the INdAM-ISIMM Workshop, Rome, Italy, September 2016 (27). Springer INdAM series, pp. 159-177. Mielke, A. and Mittnenzweig, M. (2017) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270. Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934. Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873. Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953 2016Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46. Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321). Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rate-independent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 54-69. Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The Hellinger--Kantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 2869-2911. ISSN 1095-7154 (online) Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424 Mielke, A. and Peletier, M. A. and Renger, M. (2016) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics, 41 (2). Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130). Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34. Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27. Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309. 2015Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101. Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002. Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606 Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355 Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355 Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630 Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89). Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499. Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542. |